Main Epicurve
The peak of the outbreak was reached on week 2020-W53, with a total of 3615 cases. 122 cases had missing dates, and they were excluded from the epicurves.
This document is a fake epidemiological report using data provided by the Applied Epi group using a fake COVID linelist (data available on Github).
I have used these data to create various descriptive analysis. Most of the work here is inspired from the great Epidemiologist R handbook, but also from other resources that I have used to learn R. I use pipes and all of the tidyverse has I have learned in: R for Data Science and other resources available on Rstudio website.
For data visualisation I have decided to focuss on interactive graphs using the highcharter package a wrapper for the highchart library. I have been working with highcharter for some time now but I used it as an opportunity to learn more, and apply it to a real life scenarios. I do really enjoy the adds-on of interactivity in data analysis.
For Epidemiological analysis/description I have used what I knew from the various packages regarding epi: linelist, epikit, incidence, sitrep …
For spatial analysis, I have chosen to get out of ggplot, or tmap which I have used a lot, to focuss on leaflet as it was once more an occasion to use interactivity in real life scenario for data visualisation and I think this is very powerful.
This report is more like a aggregate of data analysis and visualisation, but I have tried to stick to an epidemiologically sound structure of PERSON, TIME & PLACE.
Between the 2020-01-27 and the 2021-07-19 (a period 540 days) a total of 81979 cases have been identified, of which 82101 (100.0%) are confirmed cases.
In Fulton County, and over this period, the attack rate is of 789.06 (CI 783.89–794.26) per 10 000.
Amongst all cases of known hospitalisation status, at least 5297 (10.7%) have been hospitalised, but 32482 (39.6%) still have an unknown status
Using only cases with known outcome, the Case Fatality Ratio is of 3.37% (CI 3.20–3.55), but importantly, 123 (0.1%) cases are under review, and 42302 (51.5%) of cases missing outcome status.
Since the start of the outbreak there was, 43299 (52.7%) female cases and 38393 (46.8%) male cases.
The Age of cases ranges from 0 to 106, with Age group 20 - 30 the most represented, with 18609 (22.67%) cases.
There is 409 (0.5%) cases with missing data on Sex, and 49 (0.1%) cases with missing data on Age.
| Age group | male cases (n) | % | female cases (n) | % | unknown cases (n) | % |
|---|---|---|---|---|---|---|
| < 10 | 1423 | 3.71 | 1398 | 3.23 | 18 | 4.40 |
| 10 - 20 | 4473 | 11.65 | 4679 | 10.81 | 49 | 11.98 |
| 20 - 30 | 8280 | 21.57 | 10243 | 23.66 | 86 | 21.03 |
| 30 - 40 | 7333 | 19.10 | 8200 | 18.94 | 82 | 20.05 |
| 40 - 50 | 5949 | 15.50 | 6551 | 15.13 | 50 | 12.22 |
| 50 - 60 | 5339 | 13.91 | 5587 | 12.90 | 45 | 11.00 |
| 60 - 70 | 3126 | 8.14 | 3274 | 7.56 | 28 | 6.85 |
| 70 + | 2455 | 6.39 | 3345 | 7.73 | 39 | 9.54 |
| unknown | 15 | 0.04 | 22 | 0.05 | 12 | 2.93 |
Overall Hospitalisation rate is of 10.68% (CI 10.41–10.95), but 32482 (39.6%) still have an unknown status.
The age group, 70 + had the greatest hospitalisation rate of 44.61% (CI 43.00–46.23).
| Age groups | hospitalisations | population | Hosp. rate | 95%-CI |
|---|---|---|---|---|
| < 10 | 61 | 2005 | 3.04 | (2.38-3.89) |
| 10 - 20 | 80 | 5677 | 1.41 | (1.13-1.75) |
| 20 - 30 | 372 | 10792 | 3.45 | (3.12-3.81) |
| 30 - 40 | 575 | 9389 | 6.12 | (5.66-6.63) |
| 40 - 50 | 667 | 7603 | 8.77 | (8.16-9.43) |
| 50 - 60 | 982 | 6588 | 14.91 | (14.07-15.79) |
| 60 - 70 | 936 | 3917 | 23.90 | (22.59-25.26) |
| 70 + | 1622 | 3636 | 44.61 | (43-46.23) |
| unknown | 2 | 12 | 16.67 | (4.7-44.8) |
Hopsitalisations rates remained similar between Male ( 11.22% (CI 10.82–11.64) ) and Female ( 11.22% (CI 10.82–11.64) ).
| Sex | hospitalisations | population | Hosp. rate | 95%-CI |
|---|---|---|---|---|
| male | 2582 | 23003 | 11.22 | (10.82-11.64) |
| female | 2710 | 26524 | 10.22 | (9.86-10.59) |
| unknown | 5 | 92 | 5.43 | (2.34-12.1) |
Using only cases with known outcome, the Overall CFR is of 3.37% (CI 3.20–3.55).
Importantly, 123 (0.1%) cases are under review, while 42302 (51.5%) have unknown outcome.
| Age groups | deaths | population | CFR | 95%-CI |
|---|---|---|---|---|
| < 10 | 0 | 1620 | 0.00 | (0-0.24) |
| 10 - 20 | 1 | 4630 | 0.02 | (0-0.12) |
| 20 - 30 | 6 | 8700 | 0.07 | (0.03-0.15) |
| 30 - 40 | 27 | 7517 | 0.36 | (0.25-0.52) |
| 40 - 50 | 43 | 6086 | 0.71 | (0.52-0.95) |
| 50 - 60 | 125 | 5148 | 2.43 | (2.04-2.89) |
| 60 - 70 | 252 | 3097 | 8.14 | (7.23-9.15) |
| 70 + | 884 | 2871 | 30.79 | (29.13-32.5) |
| unknown | 0 | 7 | 0.00 | (0-35.43) |
< 10 was the age group with the lowest CFR: 0.00% (CI 0.00–0.24). While 70 + was the age group with the greatest CFR: 30.79% (CI 29.13–32.50)
| Sex | deaths | population | CFR | 95%-CI |
|---|---|---|---|---|
| male | 705 | 18440 | 3.82 | (3.56–4.11) |
| female | 633 | 21183 | 2.99 | (2.77–3.23) |
| unknown | 0 | 53 | 0.00 | (0.00–6.76) |
Amongst all cases, symptoms were distributed as follow:
| value | n | proportion |
|---|---|---|
| Fever | ||
| yes | 15127 | 18.42 |
| no | 33951 | 41.35 |
| unknown | 33023 | 40.22 |
| Subjective Fever | ||
| yes | 12712 | 15.48 |
| no | 30457 | 37.10 |
| unknown | 38932 | 47.42 |
| Myalgia | ||
| no | 29210 | 35.58 |
| yes | 19534 | 23.79 |
| unknown | 33357 | 40.63 |
| Loss of Taste & Smell | ||
| unknown | 51258 | 62.43 |
| yes | 12734 | 15.51 |
| no | 18109 | 22.06 |
| Sore throat | ||
| yes | 12516 | 15.24 |
| no | 36106 | 43.98 |
| unknown | 33479 | 40.78 |
| Cough | ||
| yes | 21943 | 26.73 |
| unknown | 32684 | 39.81 |
| no | 27474 | 33.46 |
| Headache | ||
| yes | 21675 | 26.40 |
| no | 27196 | 33.13 |
| unknown | 33230 | 40.47 |
And this was related to one another as follow:
The peak of the outbreak was reached on week 2020-W53, with a total of 3615 cases. 122 cases had missing dates, and they were excluded from the epicurves.
Cases have been detected throughout Fulton county, especially in major cities.
Below are mapped the smaller regions of Fulton county (<1000 habitants) which AR are really important (mean: 149.83) due to small size populations, mean: 306.37. This was done to allow a more nuanced mapping of other bigger regions by removing outliers.
At the peak of the outbreak: 2020-W53, the region with the greatest Attack rate was 3.0024^{4} with an Attack rate of 167.2240803 (71.63–385.42) per 10 000
Maps of big regions of Fulton county by Week of Outbreak.